System.out.println( "calculating phylogentic tree..." );
System.out.println();
phy = calcTree();
+ addSeqs2Tree( _msa, phy );
}
if ( !_realign ) {
_step = -1;
}
++i;
}
+
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, true );
displayTree( phy );
return msa_props;
}
- public final void decorateTree( final Phylogeny phy, final List<MsaProperties> msa_props, final boolean chart_only ) {
+ private final static void addSeqs2Tree( final Msa msa, final Phylogeny phy ) {
+ for( int i = 0; i < msa.getNumberOfSequences(); ++i ) {
+ final MolecularSequence seq = msa.getSequence( i );
+ final String seq_name = seq.getIdentifier();
+ final PhylogenyNode n = phy.getNode( seq_name );
+ if ( !n.getNodeData().isHasSequence() ) {
+ n.getNodeData().addSequence( new org.forester.phylogeny.data.Sequence() );
+ }
+ else {
+ throw new IllegalArgumentException( "this should not have happened" );
+ }
+ n.getNodeData().getSequence().setMolecularSequence( seq.getMolecularSequenceAsString() );
+ n.getNodeData().getSequence().setMolecularSequenceAligned( true );
+ n.getNodeData().getSequence().setName( seq_name );
+ }
+ }
+
+ private final static void decorateTree( final Phylogeny phy,
+ final List<MsaProperties> msa_props,
+ final boolean chart_only ) {
final BasicDescriptiveStatistics length_stats = new BasicDescriptiveStatistics();
for( int i = 0; i < msa_props.size(); ++i ) {
final MsaProperties msa_prop = msa_props.get( i );
config.setDisplaySequenceNames( false );
config.setDisplaySequenceSymbols( false );
config.setDisplayGeneNames( false );
+ config.setDisplayMultipleSequenceAlignment( true );
config.setShowScale( true );
config.setAddTaxonomyImagesCB( false );
config.setBaseFontSize( 9 );
System.out.println( "calculating phylogentic tree..." );
System.out.println();
phy = calcTree();
+ addSeqs2Tree( _msa, phy );
}
printTableHeader();
MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy );
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
- }
+ System.out.println( "calculating phylogentic tree..." );
+ System.out.println();
+ final Phylogeny phy2 = calcTree();
+ addSeqs2Tree( _msa, phy2 );
+ displayTree( phy2 );
+ }
+
+
return msa_props;
}
System.out.println( "calculating phylogentic tree..." );
System.out.println();
phy = calcTree();
+ addSeqs2Tree( _msa, phy );
}
printTableHeader();
MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy );
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
- }
+ System.out.println( "calculating phylogentic tree..." );
+ System.out.println();
+ final Phylogeny phy2 = calcTree();
+ addSeqs2Tree( _msa, phy2 );
+ displayTree( phy2 );
+ }
+
return msa_props;
}
System.out.println( "calculating phylogentic tree..." );
System.out.println();
phy = calcTree();
+ addSeqs2Tree( _msa, phy );
}
printTableHeader();
MsaProperties msa_prop = new MsaProperties( _msa, "", _calculate_shannon_entropy );
if ( _phylogentic_inference ) {
decorateTree( phy, msa_props, false );
displayTree( phy );
- }
+ System.out.println( "calculating phylogentic tree..." );
+ System.out.println();
+ final Phylogeny phy2 = calcTree();
+ addSeqs2Tree( _msa, phy2 );
+ displayTree( phy2 );
+ }
+
return msa_props;
}
sb.append( msa_properties.getLength() );
sb.append( "\t" );
sb.append( NF_4.format( msa_properties.getGapRatio() ) );
+ sb.append( "\t" );
+ sb.append( NF_1.format( msa_properties.getAvgNumberOfGaps() ) );
if ( _calculate_shannon_entropy ) {
sb.append( "\t" );
sb.append( NF_4.format( msa_properties.getEntropy7() ) );
System.out.print( "\t" );
System.out.print( "Length" );
System.out.print( "\t" );
+ System.out.print( "Gap R" );
+ System.out.print( "\t" );
System.out.print( "Gaps" );
System.out.print( "\t" );
if ( _calculate_shannon_entropy ) {